mailRe: r25238 - /trunk/test_suite/system_tests/relax_disp.py


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Posted by Troels Emtekær Linnet on August 25, 2014 - 16:54:
Hi Edward.

The error for r2eff seems twice as high, while i0_err are almost identical.

Best
Troels

R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 431.0.
r2eff=8.646/8.646 r2eff_err=0.0348/0.0692 i0=202664.191/202664.191
i0_err=699.6443/712.4201

R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 651.2.
r2eff=10.377/10.377 r2eff_err=0.0403/0.0810 i0=206049.558/206049.558
i0_err=776.4215/782.1833

R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 800.5.
r2eff=10.506/10.506 r2eff_err=0.0440/0.0853 i0=202586.332/202586.332
i0_err=763.9678/758.7052

R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 984.0.
r2eff=10.903/10.903 r2eff_err=0.0476/0.0922 i0=203455.021/203455.021
i0_err=837.8779/828.7280

R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1341.1.
r2eff=10.684/10.684 r2eff_err=0.0446/0.0853 i0=218670.412/218670.412
i0_err=850.0210/830.9558

R1rho at 799.8 MHz, for offset=118.078 ppm and dispersion point 1648.5.
r2eff=10.501/10.501 r2eff_err=0.0371/0.0742 i0=206502.512/206502.512
i0_err=794.0523/772.9843

R1rho at 799.8 MHz, for offset=124.247 ppm and dispersion point 1341.1.
r2eff=11.118/11.118 r2eff_err=0.0413/0.0827 i0=216447.241/216447.241
i0_err=784.6562/788.0384

R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 800.5.
r2eff=7.866/7.866 r2eff_err=0.0347/0.0695 i0=211869.715/211869.715
i0_err=749.2776/763.6930

R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1341.1.
r2eff=9.259/9.259 r2eff_err=0.0331/0.0661 i0=217703.151/217703.151
i0_err=682.2137/685.5838

R1rho at 799.8 MHz, for offset=130.416 ppm and dispersion point 1648.5.
r2eff=9.565/9.565 r2eff_err=0.0373/0.0745 i0=211988.939/211988.939
i0_err=839.0313/827.0373

R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 800.5.
r2eff=3.240/3.240 r2eff_err=0.0127/0.0253 i0=214417.382/214417.382
i0_err=595.8865/613.4378

R1rho at 799.8 MHz, for offset=142.754 ppm and dispersion point 1341.1.
r2eff=5.084/5.084 r2eff_err=0.0177/0.0352 i0=226358.691/226358.691
i0_err=660.5314/655.7670

R1rho at 799.8 MHz, for offset=179.768 ppm and dispersion point 1341.1.
r2eff=2.208/2.208 r2eff_err=0.0091/0.0178 i0=228620.553/228620.553
i0_err=564.8353/560.0873

R1rho at 799.8 MHz, for offset=241.459 ppm and dispersion point 1341.1.
r2eff=1.711/1.711 r2eff_err=0.0077/0.0155 i0=224087.486/224087.486
i0_err=539.4300/546.4217

2014-08-25 16:35 GMT+02:00 Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

Hi,

The errors from the covariance matrix estimate, via
scipy.optimize.leastsq() should be similar or even identical to the
Monte Carlo simulation errors, not double.  Is this still the case?

Regards,

Edward

On 25 August 2014 01:32,  <tlinnet@xxxxxxxxxxxxx> wrote:

Author: tlinnet
Date: Mon Aug 25 01:32:13 2014
New Revision: 25238

URL: http://svn.gna.org/viewcvs/relax?rev=25238&view=rev
Log:
Modified systemtest Relax_disp.test_estimate_r2eff.

This is to compare against errors simulated with 2000 MC.

The paramaters are comparable, but not equal.
Mostly, it seems that the errors from scipy.optimize.leastsq, are twice as 
high than the Monte Carlo simulations.
This affect model fitting, and the calculated chi2 value.

Left column is 2000 Monte Carlo, right column is scipy.optimize.leastsq.

Optimised parameters for spin: 52V @N
Model: No Rex
Parameter: r1     Value: 1.46138806 - 1.46328102
Parameter: r2     Value: 11.48392438 - 11.48040934
Parameter: chi2   Value: 848.42015672 - 3363.95829122

Model: DPL94
Parameter: r1     Value: 1.44845743 - 1.45019848
Parameter: r2     Value: 10.15688373 - 10.16304892
Parameter: phi_ex Value: 0.07599563 - 0.07561937
Parameter: kex    Value: 4460.43707304 - 4419.03906628
Parameter: chi2   Value: 179.47041255 - 710.24767560

Model: TP02
Parameter: r1     Value: 1.54354392 - 1.54352369
Parameter: r2     Value: 9.72654895 - 9.72772727
Parameter: pA     Value: 0.88827039 - 0.88807488
Parameter: dw     Value: 1.08875836 - 1.08765645
Parameter: kex    Value: 4921.28597928 - 4904.70134941
Parameter: chi2   Value: 29.33882481 - 114.47142772

Model: TAP03
Parameter: r1     Value: 1.54356410 - 1.54354368
Parameter: r2     Value: 9.72641885 - 9.72759371
Parameter: pA     Value: 0.88828925 - 0.88809317
Parameter: dw     Value: 1.08837248 - 1.08726695
Parameter: kex    Value: 4926.42974479 - 4909.86896567
Parameter: chi2   Value: 29.29050624 - 114.27987534

Model: MP05
Parameter: r1     Value: 1.54356415 - 1.54354372
Parameter: r2     Value: 9.72641730 - 9.72759220
Parameter: pA     Value: 0.88828927 - 0.88809322
Parameter: dw     Value: 1.08837250 - 1.08726707
Parameter: kex    Value: 4926.44228958 - 4909.88128236
Parameter: chi2   Value: 29.29054252 - 114.28002272

Model: NS R1rho 2-site
Parameter: r1     Value: 1.41359226 - 1.41321968
Parameter: r2     Value: 9.34531364 - 9.34602793
Parameter: pA     Value: 0.94504369 - 0.94496541
Parameter: dw     Value: 1.56001843 - 1.55833321
Parameter: kex    Value: 5628.66529504 - 5610.20221435
Parameter: chi2   Value: 34.44010458 - 134.14368365

task #7822(https://gna.org/task/index.php?7822): Implement user function 
to estimate R2eff and associated errors for exponential curve fitting.

Modified:
    trunk/test_suite/system_tests/relax_disp.py

Modified: trunk/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=25238&r1=25237&r2=25238&view=diff
==============================================================================
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Mon Aug 25 01:32:13 2014
@@ -2679,7 +2679,7 @@
         self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, 
read_R1=False)

         # The dispersion models.
-        MODELS = [MODEL_NOREX, MODEL_DPL94]
+        MODELS = [MODEL_NOREX, MODEL_DPL94, MODEL_TP02, MODEL_TAP03, 
MODEL_MP05, MODEL_NS_R1RHO_2SITE]

         # The grid search size (the number of increments per dimension).
         GRID_INC = None
@@ -2723,6 +2723,9 @@

         # Run the analysis.
         relax_disp.Relax_disp(pipe_name=ds.pipe_name, 
pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, 
grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL)
+
+        # Verify the data.
+        self.verify_r1rho_kjaergaard_missing_r1(models=MODELS, 
result_dir_name=result_dir_name, do_assert=False)


     def test_exp_fit(self):
@@ -7343,7 +7346,7 @@
         w_eff_file.close()


-    def verify_r1rho_kjaergaard_missing_r1(self, models=None, 
result_dir_name=None):
+    def verify_r1rho_kjaergaard_missing_r1(self, models=None, 
result_dir_name=None, do_assert=True):
         """Verification of test_r1rho_kjaergaard_missing_r1."""

         # Check the kex value of residue 52
@@ -7382,35 +7385,36 @@
                             # Print value.
                             print("%-10s %-6s %-6s %3.8f" % 
("Parameter:", param, "Value:", value))

-                            # Compare values.
-                            if spin_id == ':52@N':
-                                if param == 'r1':
-                                    if model == MODEL_NOREX:
-                                        self.assertAlmostEqual(value, 
1.46328102)
-                                    elif model == MODEL_DPL94:
-                                        self.assertAlmostEqual(value, 
1.45019848)
-                                    elif model == MODEL_TP02:
-                                        self.assertAlmostEqual(value, 
1.54352369)
-                                    elif model == MODEL_TAP03:
-                                        self.assertAlmostEqual(value, 
1.54354367)
-                                    elif model == MODEL_MP05:
-                                        self.assertAlmostEqual(value, 
1.54354372)
-                                    elif model == MODEL_NS_R1RHO_2SITE:
-                                        self.assertAlmostEqual(value, 
1.41321968, 6)
-
-                                elif param == 'r2':
-                                    if model == MODEL_NOREX:
-                                        self.assertAlmostEqual(value, 
11.48040934)
-                                    elif model == MODEL_DPL94:
-                                        self.assertAlmostEqual(value, 
10.16304887, 6)
-                                    elif model == MODEL_TP02:
-                                        self.assertAlmostEqual(value, 
9.72772726, 6)
-                                    elif model == MODEL_TAP03:
-                                        self.assertAlmostEqual(value, 
9.72759374, 6)
-                                    elif model == MODEL_MP05:
-                                        self.assertAlmostEqual(value, 
9.72759220, 6)
-                                    elif model == MODEL_NS_R1RHO_2SITE:
-                                        self.assertAlmostEqual(value, 
9.34602793, 5)
+                            if do_assert:
+                                # Compare values.
+                                if spin_id == ':52@N':
+                                    if param == 'r1':
+                                        if model == MODEL_NOREX:
+                                            self.assertAlmostEqual(value, 
1.46328102)
+                                        elif model == MODEL_DPL94:
+                                            self.assertAlmostEqual(value, 
1.45019848)
+                                        elif model == MODEL_TP02:
+                                            self.assertAlmostEqual(value, 
1.54352369)
+                                        elif model == MODEL_TAP03:
+                                            self.assertAlmostEqual(value, 
1.54354367)
+                                        elif model == MODEL_MP05:
+                                            self.assertAlmostEqual(value, 
1.54354372)
+                                        elif model == 
MODEL_NS_R1RHO_2SITE:
+                                            self.assertAlmostEqual(value, 
1.41321968, 6)
+
+                                    elif param == 'r2':
+                                        if model == MODEL_NOREX:
+                                            self.assertAlmostEqual(value, 
11.48040934)
+                                        elif model == MODEL_DPL94:
+                                            self.assertAlmostEqual(value, 
10.16304887, 6)
+                                        elif model == MODEL_TP02:
+                                            self.assertAlmostEqual(value, 
9.72772726, 6)
+                                        elif model == MODEL_TAP03:
+                                            self.assertAlmostEqual(value, 
9.72759374, 6)
+                                        elif model == MODEL_MP05:
+                                            self.assertAlmostEqual(value, 
9.72759220, 6)
+                                        elif model == 
MODEL_NS_R1RHO_2SITE:
+                                            self.assertAlmostEqual(value, 
9.34602793, 5)

                     # For all other parameters.
                     else:
@@ -7420,57 +7424,58 @@
                         # Print value.
                         print("%-10s %-6s %-6s %3.8f" % ("Parameter:", 
param, "Value:", value))

-                        # Compare values.
-                        if spin_id == ':52@N':
-                            if param == 'phi_ex':
-                                if model == MODEL_DPL94:
-                                    self.assertAlmostEqual(value, 
0.07561937)
-
-                            elif param == 'pA':
-                                if model == MODEL_TP02:
-                                    self.assertAlmostEqual(value, 
0.88807487)
-                                elif model == MODEL_TAP03:
-                                    self.assertAlmostEqual(value, 
0.88809318)
-                                elif model == MODEL_MP05:
-                                    self.assertAlmostEqual(value, 
0.88809321)
-                                elif model == MODEL_NS_R1RHO_2SITE:
-                                    self.assertAlmostEqual(value, 
0.94496541, 6)
-
-                            elif param == 'dw':
-                                if model == MODEL_TP02:
-                                    self.assertAlmostEqual(value, 
1.08765638, 6)
-                                elif model == MODEL_TAP03:
-                                    self.assertAlmostEqual(value, 
1.08726698, 6)
-                                elif model == MODEL_MP05:
-                                    self.assertAlmostEqual(value, 
1.08726706, 6)
-                                elif model == MODEL_NS_R1RHO_2SITE:
-                                    self.assertAlmostEqual(value, 
1.55833321, 5)
-
-                            elif param == 'kex':
-                                if model == MODEL_DPL94:
-                                    self.assertAlmostEqual(value, 
4419.03917195, 2)
-                                elif model == MODEL_TP02:
-                                    self.assertAlmostEqual(value, 
4904.70144883, 3)
-                                elif model == MODEL_TAP03:
-                                    self.assertAlmostEqual(value, 
4909.86877150, 3)
-                                elif model == MODEL_MP05:
-                                    self.assertAlmostEqual(value, 
4909.88110195, 3)
-                                elif model == MODEL_NS_R1RHO_2SITE:
-                                    self.assertAlmostEqual(value, 
5610.20221435, 2)
-
-                            elif param == 'chi2':
-                                if model == MODEL_NOREX:
-                                    self.assertAlmostEqual(value, 
3363.95829122)
-                                elif model == MODEL_DPL94:
-                                    self.assertAlmostEqual(value, 
710.24767560)
-                                elif model == MODEL_TP02:
-                                    self.assertAlmostEqual(value, 
114.47142772)
-                                elif model == MODEL_TAP03:
-                                    self.assertAlmostEqual(value, 
114.27987534)
-                                elif model == MODEL_MP05:
-                                    self.assertAlmostEqual(value, 
114.28002272)
-                                elif model == MODEL_NS_R1RHO_2SITE:
-                                    self.assertAlmostEqual(value, 
134.14368365)
+                        if do_assert:
+                            # Compare values.
+                            if spin_id == ':52@N':
+                                if param == 'phi_ex':
+                                    if model == MODEL_DPL94:
+                                        self.assertAlmostEqual(value, 
0.07561937)
+
+                                elif param == 'pA':
+                                    if model == MODEL_TP02:
+                                        self.assertAlmostEqual(value, 
0.88807487)
+                                    elif model == MODEL_TAP03:
+                                        self.assertAlmostEqual(value, 
0.88809318)
+                                    elif model == MODEL_MP05:
+                                        self.assertAlmostEqual(value, 
0.88809321)
+                                    elif model == MODEL_NS_R1RHO_2SITE:
+                                        self.assertAlmostEqual(value, 
0.94496541, 6)
+
+                                elif param == 'dw':
+                                    if model == MODEL_TP02:
+                                        self.assertAlmostEqual(value, 
1.08765638, 6)
+                                    elif model == MODEL_TAP03:
+                                        self.assertAlmostEqual(value, 
1.08726698, 6)
+                                    elif model == MODEL_MP05:
+                                        self.assertAlmostEqual(value, 
1.08726706, 6)
+                                    elif model == MODEL_NS_R1RHO_2SITE:
+                                        self.assertAlmostEqual(value, 
1.55833321, 5)
+
+                                elif param == 'kex':
+                                    if model == MODEL_DPL94:
+                                        self.assertAlmostEqual(value, 
4419.03917195, 2)
+                                    elif model == MODEL_TP02:
+                                        self.assertAlmostEqual(value, 
4904.70144883, 3)
+                                    elif model == MODEL_TAP03:
+                                        self.assertAlmostEqual(value, 
4909.86877150, 3)
+                                    elif model == MODEL_MP05:
+                                        self.assertAlmostEqual(value, 
4909.88110195, 3)
+                                    elif model == MODEL_NS_R1RHO_2SITE:
+                                        self.assertAlmostEqual(value, 
5610.20221435, 2)
+
+                                elif param == 'chi2':
+                                    if model == MODEL_NOREX:
+                                        self.assertAlmostEqual(value, 
3363.95829122)
+                                    elif model == MODEL_DPL94:
+                                        self.assertAlmostEqual(value, 
710.24767560)
+                                    elif model == MODEL_TP02:
+                                        self.assertAlmostEqual(value, 
114.47142772)
+                                    elif model == MODEL_TAP03:
+                                        self.assertAlmostEqual(value, 
114.27987534)
+                                    elif model == MODEL_MP05:
+                                        self.assertAlmostEqual(value, 
114.28002272)
+                                    elif model == MODEL_NS_R1RHO_2SITE:
+                                        self.assertAlmostEqual(value, 
134.14368365)


         # Print the final pipe.
@@ -7524,7 +7529,7 @@

                 # Assign the split of the line.
                 mol_name, res_num, res_name, spin_num, spin_name, val, 
sd_error = line_split
-                print mol_name, res_num, res_name, spin_num, spin_name, 
val, sd_error
+                print(mol_name, res_num, res_name, spin_num, spin_name, 
val, sd_error)

                 if res_num == '52':
                     # Assert that the value is not None.


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